SMTL ID : 5w97.1

Crystal Structure of CO-bound Cytochrome c Oxidase determined by Serial Femtosecond X-Ray Crystallography at Room Temperature

HEA.1: 35 residues within 4Å: Chain A: G.27, M.28, T.31, S.34, I.37, R.38, Y.54, V.58, H.61, A.62, M.65, I.66, M.69, V.70, I.73, G.125, W.126, Y.371, V.374, F.377, H.378, L.381, S.382, V.386, M.390, F.393, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, V.465, M.468 33 PLIP interactions: 33 interactions with chain A, Hydrophobic interactions: A:T.31, A:A.62, A:M.65, A:I.66, A:V.70, A:V.374, A:F.377, A:F.377, A:L.381, A:L.381, A:V.386, A:F.393, A:T.424, A:F.425, A:F.425, A:V.465 Hydrogen bonds: A:S.34, A:S.34, A:R.38, A:Y.54, A:W.126, A:R.439, A:Y.440 Water bridges: A:R.438, A:R.438, A:S.461, A:S.461 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:F.425 pi-Cation interactions: A:H.378 Metal complexes: A:H.61, A:H.378 HEA.2: 34 residues within 4Å: Chain A: W.126, W.236, V.243, Y.244, I.247, H.290, H.291, T.309, I.312, A.313, T.316, G.317, V.320, F.348, T.349, G.352, L.353, G.355, I.356, L.358, A.359, D.364, H.368, V.373, H.376, F.377, V.380, L.381, R.438 Chain B: I.34, P.69, I.72, L.73 Ligands: CMO.9 35 PLIP interactions: 30 interactions with chain A, 4 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.236, A:V.243, A:V.243, A:I.247, A:I.247, A:T.309, A:T.316, A:V.320, A:F.348, A:L.353, A:I.356, A:L.358, A:L.358, A:V.373, A:F.377, A:F.377, A:V.380, A:L.381, A:L.381, A:L.381, B:I.34, B:I.34, B:I.72, B:L.73 Hydrogen bonds: A:W.126, A:Y.244, A:Y.244 Water bridges: A:D.369, A:D.369, A:R.438, A:R.439 Salt bridges: A:H.368, A:R.438 Metal complexes: A:H.376, CMO.9 HEA.30: 30 residues within 4Å: Chain N: M.28, T.31, S.34, I.37, R.38, Y.54, V.58, H.61, A.62, M.65, I.66, M.69, V.70, G.125, W.126, Y.371, V.374, F.377, H.378, L.381, V.386, F.393, T.424, F.425, Q.428, R.438, R.439, Y.440, V.465, M.468 36 PLIP interactions: 36 interactions with chain N, Hydrophobic interactions: N:T.31, N:V.58, N:V.58, N:A.62, N:M.65, N:I.66, N:V.70, N:V.374, N:F.377, N:L.381, N:L.381, N:V.386, N:V.386, N:F.393, N:T.424, N:F.425, N:F.425, N:F.425, N:V.465 Hydrogen bonds: N:S.34, N:S.34, N:R.38, N:W.126, N:Y.371, N:Q.428, N:R.439, N:Y.440 Water bridges: N:R.438, N:R.438 Salt bridges: N:R.438, N:R.439 pi-Stacking: N:F.377, N:H.378, N:F.425 Metal complexes: N:H.61, N:H.378 HEA.31: 32 residues within 4Å: Chain N: W.126, W.236, V.243, Y.244, I.247, H.290, H.291, T.309, I.312, A.313, T.316, G.317, T.349, G.352, L.353, G.355, I.356, L.358, A.359, D.364, H.368, V.373, H.376, F.377, V.380, L.381, R.438 Chain O: I.34, P.69, I.72, L.73 Ligands: CMO.37 34 PLIP interactions: 30 interactions with chain N, 3 interactions with chain O, 1 Ligand-Ligand interactions Hydrophobic interactions: N:W.236, N:V.243, N:V.243, N:I.247, N:I.247, N:T.309, N:T.316, N:T.349, N:L.353, N:I.356, N:L.358, N:V.373, N:F.377, N:F.377, N:V.380, N:L.381, N:L.381, N:L.381, O:I.34, O:I.72, O:L.73 Hydrogen bonds: N:W.126, N:Y.244 Water bridges: N:T.316, N:D.369, N:D.369, N:R.438, N:R.439 Salt bridges: N:H.368, N:R.438, N:R.439 pi-Cation interactions: N:H.240 Metal complexes: N:H.376, CMO.37

CU.3: 4 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: CMO.9 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.240, A:H.290, A:H.291, CMO.9 CU.32: 4 residues within 4Å: Chain N: H.240, H.290, H.291 Ligands: CMO.37 4 PLIP interactions: 3 interactions with chain N, 1 Ligand-Ligand interactions Metal complexes: N:H.240, N:H.290, N:H.291, CMO.37

MG.4: 3 residues within 4Å: Chain A: H.368, D.369 Chain B: E.198 6 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:E.198, A:H.368, A:D.369, H2O.9, H2O.9, H2O.11 MG.33: 4 residues within 4Å: Chain N: H.368, D.369 Chain O: D.173, E.198 5 PLIP interactions: 2 interactions with chain N, 1 interactions with chain O, 2 Ligand-Water interactions Metal complexes: N:H.368, N:D.369, O:E.198, H2O.39, H2O.39

NA.5: 5 residues within 4Å: Chain A: E.40, Q.43, G.45, S.441, D.442 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.45 Water bridges: A:Q.43 NA.34: 5 residues within 4Å: Chain N: E.40, Q.43, G.45, S.441, D.442 3 PLIP interactions: 3 interactions with chain N Hydrogen bonds: N:E.40, N:D.442, N:D.442

PGV.6: 13 residues within 4Å: Chain A: N.406, T.408, W.409 Chain D: T.80, A.84, F.87 Chain K: F.9, H.10 Chain M: P.12, Q.15, A.16, L.19, S.20 11 PLIP interactions: 3 interactions with chain A, 1 interactions with chain K, 4 interactions with chain M, 3 interactions with chain D Hydrophobic interactions: A:T.408, A:W.409, A:W.409, K:F.9, M:P.12, M:P.12, M:A.16, M:L.19, D:T.80, D:A.84, D:F.87 PGV.7: 24 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, L.152 Chain C: H.9, V.11, A.24, L.31, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, F.86, S.89, E.90 Ligands: PEK.14, PGV.15 14 PLIP interactions: 5 interactions with chain A, 9 interactions with chain C Hydrophobic interactions: A:L.152, C:A.24, C:L.31, C:W.57, C:W.57, C:W.58, C:F.86, C:E.90 Hydrogen bonds: A:R.96, A:R.96, A:M.97, C:H.9, C:H.71 Salt bridges: A:R.96 PGV.15: 21 residues within 4Å: Chain C: M.54, W.58, V.61, S.65, T.66, H.71, M.83, H.207, I.210, T.213, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234 Ligands: PGV.7, CDL.17 21 PLIP interactions: 20 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:W.58, C:W.58, C:W.58, C:W.58, C:I.210, C:I.210, C:T.213, C:F.214, C:F.214 Hydrogen bonds: C:S.65, C:T.66, C:R.221, C:F.233, C:G.234 Water bridges: C:R.221, C:H.231, C:H.231, F:E.17 Salt bridges: C:R.221, C:R.221, C:H.231 PGV.16: 12 residues within 4Å: Chain A: D.298 Chain C: T.95, W.99, Y.102, H.103, A.107 Chain H: N.22 Chain P: W.258 Chain T: A.1, S.2 Ligands: CHD.13, PEK.21 8 PLIP interactions: 2 interactions with chain A, 3 interactions with chain H, 3 interactions with chain C Water bridges: A:D.298, A:D.298, H:N.22 Hydrogen bonds: H:N.22, H:N.24 Hydrophobic interactions: C:T.95, C:W.99, C:W.99 PGV.26: 9 residues within 4Å: Chain C: W.258, W.259 Chain G: A.1 Chain P: T.95, W.99, H.103, L.106 Ligands: CDL.24, CHD.41 8 PLIP interactions: 4 interactions with chain C, 1 interactions with chain N, 3 interactions with chain P Hydrophobic interactions: C:W.258, C:W.258, C:W.258, C:W.259, P:W.99, P:W.99, P:W.99 Hydrogen bonds: N:D.298 PGV.36: 11 residues within 4Å: Chain N: N.406, T.408, W.409 Chain Q: T.80, A.84, F.87 Chain X: F.9, H.10 Chain Z: A.3, K.4, Q.15 8 PLIP interactions: 2 interactions with chain N, 2 interactions with chain Q, 2 interactions with chain Z, 2 interactions with chain X Hydrophobic interactions: N:T.408, N:W.409, Q:A.84, Q:F.87, X:F.9 Hydrogen bonds: Z:K.4 Water bridges: Z:A.6 Salt bridges: X:H.10 PGV.40: 22 residues within 4Å: Chain N: F.94, P.95, R.96, M.97, M.100, V.155, I.158 Chain P: H.9, T.28, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, F.86, F.93 Ligands: PGV.43, PEK.49 15 PLIP interactions: 9 interactions with chain P, 6 interactions with chain N Hydrophobic interactions: P:T.28, P:W.57, P:W.57, P:W.58, P:F.86, P:F.93, N:V.155, N:I.158 Hydrogen bonds: P:H.9, P:W.57, P:E.64, N:R.96, N:M.97 Water bridges: N:A.93 Salt bridges: N:R.96 PGV.43: 20 residues within 4Å: Chain P: M.54, W.58, V.61, S.65, T.66, H.71, F.86, I.210, T.213, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234 Ligands: PGV.40, CDL.44 26 PLIP interactions: 24 interactions with chain P, 2 interactions with chain S Hydrophobic interactions: P:W.58, P:W.58, P:W.58, P:W.58, P:F.86, P:F.86, P:I.210, P:T.213, P:F.214, P:F.214, P:F.214, P:F.214 Hydrogen bonds: P:S.65, P:H.71, P:R.221, P:F.233, P:G.234 Water bridges: P:S.65, P:R.221, P:H.231, P:H.231, S:Q.12, S:E.17 Salt bridges: P:R.221, P:R.221, P:H.231

TGL.8: 14 residues within 4Å: Chain A: V.350, N.422, F.426, F.430, L.433 Chain B: L.7, G.8, H.24, L.28, V.31, F.32, S.35, L.39 Chain I: R.43 10 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A, 1 interactions with chain I Hydrophobic interactions: B:V.31, B:F.32, B:F.32, B:L.39, A:V.350, A:N.422, A:F.426, A:F.430 Salt bridges: B:H.24, I:R.43 TGL.22: 14 residues within 4Å: Chain A: I.332, W.334, M.339, K.411, F.414, A.415 Chain B: L.46, T.47, T.48 Chain D: R.73, E.77, W.78, V.81 Chain I: R.16 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:V.81, A:W.334, A:W.334, A:F.414 Water bridges: D:W.78 Salt bridges: A:K.411 TGL.28: 18 residues within 4Å: Chain A: F.2, L.7, T.17, L.21, F.22, W.25, F.393, F.400, I.472 Chain L: N.10, I.11, P.12, F.13, R.20, M.25, F.28, F.29, S.31 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain L Hydrophobic interactions: A:L.21, A:F.22, A:F.22, A:W.25, A:F.393, A:I.472, L:I.11, L:F.13, L:F.28, L:F.28, L:F.29 TGL.35: 13 residues within 4Å: Chain N: W.334, M.339, K.411 Chain O: I.42, L.46 Chain Q: N.72, R.73, T.75, E.77, W.78, V.81 Chain V: R.16, H.20 9 PLIP interactions: 4 interactions with chain N, 2 interactions with chain O, 3 interactions with chain Q Hydrophobic interactions: N:W.334, N:W.334, N:K.411, O:I.42, O:L.46, Q:W.78, Q:V.81 Salt bridges: N:K.411 Hydrogen bonds: Q:W.78 TGL.51: 14 residues within 4Å: Chain N: V.350, N.422, F.426, F.430, L.433 Chain O: L.7, G.8, H.24, L.28, F.32, S.35, L.39 Chain V: F.31, R.43 8 PLIP interactions: 3 interactions with chain O, 3 interactions with chain N, 2 interactions with chain V Hydrophobic interactions: O:L.28, O:F.32, N:V.350, N:F.426, N:F.430, V:F.31 Salt bridges: O:H.24, V:R.43 TGL.53: 16 residues within 4Å: Chain N: F.2, L.7, T.17, L.18, L.21, L.113, F.400, I.472 Chain Y: I.11, P.12, F.13, S.14, M.24, M.25, F.28, F.29 14 PLIP interactions: 6 interactions with chain N, 8 interactions with chain Y Hydrophobic interactions: N:F.2, N:T.17, N:L.18, N:L.113, N:F.400, N:I.472, Y:I.11, Y:F.13, Y:F.13, Y:F.28, Y:F.28, Y:F.28, Y:F.29, Y:F.29

CMO.9: 7 residues within 4Å: Chain A: H.240, V.243, H.290, H.291, H.376 Ligands: HEA.2, CU.3 No protein-ligand interaction detected (PLIP) CMO.37: 7 residues within 4Å: Chain N: H.240, V.243, H.290, H.291, H.376 Ligands: HEA.31, CU.32 No protein-ligand interaction detected (PLIP)

CUA.10: 6 residues within 4Å: Chain B: H.161, C.196, E.198, C.200, H.204, M.207 7 PLIP interactions: 7 interactions with chain B Metal complexes: B:H.161, B:C.196, B:C.196, B:E.198, B:C.200, B:C.200, B:H.204 CUA.39: 6 residues within 4Å: Chain O: H.161, C.196, E.198, C.200, H.204, M.207 7 PLIP interactions: 7 interactions with chain O Metal complexes: O:H.161, O:C.196, O:C.196, O:E.198, O:C.200, O:C.200, O:H.204

PSC.11: 15 residues within 4Å: Chain A: F.321, A.325, H.328 Chain B: H.52, M.56, D.57, E.60, W.65 Chain E: D.8, F.11, L.41 Chain I: L.17, R.18, I.21, F.25 10 PLIP interactions: 4 interactions with chain I, 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: I:L.17, I:I.21, I:F.25, A:F.321, A:F.321, A:A.325, B:W.65, B:W.65 Salt bridges: I:R.18 Hydrogen bonds: B:D.57 PSC.47: 15 residues within 4Å: Chain N: F.321, A.325, H.328 Chain O: I.41, H.52, T.55, D.57, E.60, V.61, I.64 Chain R: H.5, E.6, T.7, D.8 Chain V: L.17 5 PLIP interactions: 3 interactions with chain O, 1 interactions with chain N, 1 interactions with chain R Hydrophobic interactions: O:I.41, O:V.61, O:I.64, N:F.321 Salt bridges: R:D.8

CHD.12: 12 residues within 4Å: Chain A: M.271, G.272, W.275 Chain B: Q.59, E.62, T.63, T.66 Chain T: R.14, R.17, F.18, F.21, G.22 10 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A, 3 interactions with chain T Hydrogen bonds: B:E.62, B:E.62, B:T.63 Hydrophobic interactions: A:M.271, A:W.275, A:W.275, A:W.275, T:F.18 Salt bridges: T:R.14, T:R.17 CHD.13: 10 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304 Chain C: W.99, H.103 Chain P: L.127 Ligands: PGV.16, CDL.50 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:W.288, A:Y.304 Hydrogen bonds: A:T.301, C:W.99 Salt bridges: A:H.233, C:H.103 CHD.18: 6 residues within 4Å: Chain C: R.156, K.157, L.160, F.164, L.223 Chain J: F.1 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:K.157, C:L.160, C:F.164, C:F.164, C:L.223 Salt bridges: C:R.156 Hydrogen bonds: J:F.1 CHD.27: 5 residues within 4Å: Chain J: Y.32, R.33, M.36, T.37, L.40 3 PLIP interactions: 3 interactions with chain J